This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Recent progress in the development of fluorescence microscopes based on micro-optics and micro-mechanical actuators now allows fluorescence imaging in the brains of freely moving animals. This involves miniaturized one- and two-photon fluorescence microscopes of about two grams in mass, light enough to be borne on the head of a freely moving adult mouse. Our lab (the Schnitzer lab at Stanford) has created miniaturized microscopes of both varieties and is now imaging microcirculation, neuronal activity, and glial dynamics in freely moving mice. In order to integrate the information obtained from live animals using these capabilities with multiscale atlases, from the cell level to tissue organization, we will work with the NCMIR and the imaging technologies and database systems they are developing to align dynamic observation data with 3Dmicroanatomy.